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John Deck edited this page Jan 26, 2023 · 52 revisions

Welcome to the home of the Biocode LIMS (Laboratory Information Management) Software. The Biocode LIMS software operates as a plugin to the Geneious software and comprises everything you need to manage your lab and sequence analysis workflows. This wiki serves both as a repository for the plugins themselves (with release notes and links to downloads), and an extensive online manual. You can download the plugin by jumping to the Downloading section below.

You can also learn about the Biocode LIMS by reading the Laboratory Information Management Systems for DNA Barcoding article published in Methods In Molecular Biology

Table of Contents

  1. Downloading
  2. Automatic Updates
  3. Getting Help
  4. LIMS
  5. Assembly
  6. Analysis
  7. Reporting
  8. Submission
  9. FIMS Annotation
  10. LIMS Plugin Release Instructions
  11. LIMS Server

Downloading

By downloading and installing these plugins, you agree to the terms of use.

Automatic Updates

You will want to be notified when the Biocode Plugin is updated so you can stay on top of bug and feature improvements to the plugin. Go to Tools → Preferences → General, and click “Advanced…”. Look for the advanced preference CustomPluginXmlUrl. Select it, click Edit and enter the following address:

https://raw.githubusercontent.com/biocodellc/biocode-lims/develop/DownloadablePlugins.xml

You will need to restart Geneious for your changes to take affect. The next time a biocode plugin is released, you will be notified to install it when you start Geneious.

Getting Help

The Biocode LIMS plugin is complex, and while learning how to use it can seem like a daunting task, help is available. Your first port of call should be the introduction video, which walks you through how to use the Biocode LIMS plugin.

If you have and questions or suggestions that you don't want to post to the community, you can email [email protected]

LIMS

  • Key Concepts - Key concepts that you need to know before using the biocode plugin.
  • Workflows - It is important that you understand how workflows work before entering data.
  • Entering Data - How to enter data into the LIMS, from your first plate through to cherry picking failed reactions for a second try.
  • Searching- How to intelligently search your data in the LIMS
  • Collating Workflows - Workflows can be combined into summary views for project managers and troubleshooters.
  • Printing- All views of the LIMS data are fully printable. This section explains how to get the most out of printing.
  • Export - The biocode plugin supports exporting plates and summary views to excel, as well as a selection of other formats.
  • Creating-a-Mysql-LIMS-Database - Information on creating a shared mysql database to store your LIMS data.

Assembly

  • Assembly Workflow - A flow diagram describing the full assembly workflow.
  • Importing Trace Data - How to get your trace data into Geneious.
  • Binning - Group your traces/contigs based on overall quality to speed up the assembly workflow, and quickly identify problem sequences.
  • Trimming - Trim low quality data and primers from the ends of your sequences.
  • Mark as Pass/Fail - Mark sequences as having passed or failed in the LIMS
  • Assembly - Assembling the prepared reads into contigs.

Analysis

Reporting

Submission

FIMS Annotation

LIMS Plugin Release Instructions

Instructions for developers working on release targets for the LIMS plugin are contained in a release checklist.

LIMS Server

This repository contains the code to run the LIMS Server. The LIMS server is a beta product that can ease connections to the LIMS database and act as an interface to a multi-purpose LIMS backend. Additional information can be found on the LIMS Server wiki page

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